I'm not sure what the "correct" answer is. I "think" if you use wire cutters, diagonal cutters (diags/*) they would not give you a clean exit for the wire inside. Others may be able to confirm this would work. If you are left with a burr or "tag" sticking out interfering with the inner wire, you could also use a small rat tail file to reshape the exit.
What I did was use a cut-off wheel on my Dremel. I measured first. I already had the spark plug wires and throttle linkage installed. I wanted to see what was in the way before figuring out how much to cut. I routed to give both a nice non-binding arc to the carb bracket.
Pull the inner wires way back out of the way before cutting. After install, then you can measure the inner wires to the correct length.
Both inner and outer cuts, take your time and measure multiple times to ensure you're happy with the length. After the cut, you can't go back and fix it.